Mullooly wrote Saint Clement, Pope and Martyr, and His Basilica in Rome about the excavation project at San Clemente. "Mullooly’s courage and desire to preserve ancient artifacts can be noted in his defense of the Basilica of San Clemente from destruction. When Garibaldi’s revolutionary forces took over Rome in 1848, Mullooly defended his church even after the Pope fled the Vatican".[3]

Princess Alice of Great Britain and Ireland and later Grand Duchess of Hesse mentions in a letter dated 9th April 1873 to her mother, Queen Victoria, that Joseph Mullooly had shown her around San Clemente during her visit to Rome in April 1873: "We visited San Clemente two days ago, and Father Mulooly [sic] took us through the three churches - one under the other"[4]